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core::pack::interaction_graph::SymmOnTheFlyEdge Class Referenceabstract

#include <SymmOnTheFlyInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::SymmOnTheFlyEdge:
Inheritance graph
[legend]

Public Member Functions

 ~SymmOnTheFlyEdge () override
 
 SymmOnTheFlyEdge (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)
 
void add_ProCorrection_values (int node_not_necessarily_proline, int state, core::PackerEnergy bb_nonprobb_E, core::PackerEnergy bb_probb_E, core::PackerEnergy sc_nonprobb_E, core::PackerEnergy sc_probb_E)
 
void add_GlyCorrection_values (int node_not_necessarily_glycine, int state, core::PackerEnergy bb_nonglybb_E, core::PackerEnergy bb_glybb_E, core::PackerEnergy sc_nonglybb_E, core::PackerEnergy sc_glybb_E)
 
core::PackerEnergy get_proline_correction_for_node (int node_ind, int state) const
 
core::PackerEnergy get_glycine_correction_for_node (int node_ind, int state) const
 
unsigned int count_static_memory () const override=0
 
unsigned int count_dynamic_memory () const override
 
bool long_range_interactions_exist () const
 
bool short_range_interactions_exist () const
 
void note_long_range_interactions_exist ()
 
void note_short_range_interactions_exist ()
 
ResiduePairEvalType eval_type (int node_index) const
 
void set_residues_adjacent_for_subunit_pair (int which_node, int other_node_subunit)
 
unsigned char residues_adjacent_for_subunit_pair (int which_node, int other_node_subunit, int whichnode_restypegroup, int othernode_restypegroup) const
 
void set_sparse_aa_info (ObjexxFCL::FArray2_bool const &) override
 fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop. More...
 
bool get_sparse_aa_info (int, int) const override
 fullfilling base class virtual member request – however, this function does not quite make sense for a symmetric otf ig, so this is just stubbed out to return true. More...
 
void force_aa_neighbors (int, int) override
 fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop. More...
 
void force_all_aa_neighbors () override
 fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop. More...
 
core::PackerEnergy get_two_body_energy (int const, int const ) const override=0
 
- Public Member Functions inherited from core::pack::interaction_graph::FixedBBEdge
 ~FixedBBEdge () override
 
 FixedBBEdge (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)
 
- Public Member Functions inherited from core::pack::interaction_graph::EdgeBase
virtual ~EdgeBase ()
 copy constructor, do not use More...
 
 EdgeBase (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)
 main constructor for edge, no default nor copy constructors More...
 
int get_other_ind (int callers_index) const
 returns the index of the other node that the edge is incident upon More...
 
NodeBaseget_other_node (int callers_index) const
 returns a pointer to the other node that the edge is incident upon More...
 
int get_first_node_ind () const
 returns the index of the smaller-indexed node More...
 
int get_second_node_ind () const
 returns the index of the larger-indexed node More...
 
void set_pos_in_owners_list (std::list< EdgeBase * >::iterator edge_iterator)
 edge keeps iterator to its position in it's owner's edge list More...
 
void set_pos_in_node_edgevector (int callers_index, int position)
 edge keeps index it has in node_ind's edge vector More...
 
bool same_edge (int node1, int node2) const
 returns true if this edge connects nodes of index node1 and node2 the order of node1 and node2 is not important More...
 
virtual void declare_energies_final ()=0
 
virtual void prepare_for_simulated_annealing ()=0
 
Real edge_weight () const
 
virtual void set_edge_weight (Real weight)=0
 
bool marked_for_deletion () const
 Has this edge indicated that it can be deleted? More...
 
InteractionGraphBase const * get_owner () const
 
InteractionGraphBaseget_owner ()
 

Protected Member Functions

core::PackerEnergy get_proline_correction (int which_node, int state) const
 
core::PackerEnergy get_glycine_correction (int which_node, int state) const
 
SymmOnTheFlyNode const * get_otf_node (int which_node) const
 
SymmOnTheFlyNodeget_otf_node (int which_node)
 
SymmOnTheFlyInteractionGraph
const * 
get_otf_owner () const
 
SymmOnTheFlyInteractionGraphget_otf_owner ()
 
- Protected Member Functions inherited from core::pack::interaction_graph::EdgeBase
void mark_edge_for_deletion ()
 Mark this edge so that it can be deleted. More...
 
int get_node_index (int index) const
 
int get_num_states_for_node (int index) const
 
NodeBase const * get_node (int index) const
 
NodeBaseget_node (int index)
 
int get_edges_position_in_nodes_edge_vector (int index) const
 
int which_node (int node_index) const
 is a node the first or second node this edge is incident upon? More...
 
void edge_weight (Real)
 protected setter of the edge weight. To be called by derived classes after they have completed the conversion from the previous edge weighting to the new edge weighting. More...
 

Private Attributes

ObjexxFCL::FArray4D< unsigned
char > 
restypegroup_adjacency_
 
utility::vector1
< core::PackerEnergy
proline_corrections_ [2]
 
utility::vector1
< core::PackerEnergy
glycine_corrections_ [2]
 
ResiduePairEvalType eval_types_ [2]
 
bool long_range_interactions_exist_
 
bool short_range_interactions_exist_
 

Constructor & Destructor Documentation

core::pack::interaction_graph::SymmOnTheFlyEdge::~SymmOnTheFlyEdge ( )
overridedefault
core::pack::interaction_graph::SymmOnTheFlyEdge::SymmOnTheFlyEdge ( InteractionGraphBase owner,
int  first_node_ind,
int  second_node_ind 
)

Member Function Documentation

void core::pack::interaction_graph::SymmOnTheFlyEdge::add_GlyCorrection_values ( int  node_not_necessarily_glycine,
int  state,
core::PackerEnergy  bb_nonglybb_E,
core::PackerEnergy  bb_glybb_E,
core::PackerEnergy  sc_nonglybb_E,
core::PackerEnergy  sc_glybb_E 
)
void core::pack::interaction_graph::SymmOnTheFlyEdge::add_ProCorrection_values ( int  node_not_necessarily_proline,
int  state,
core::PackerEnergy  bb_nonprobb_E,
core::PackerEnergy  bb_probb_E,
core::PackerEnergy  sc_nonprobb_E,
core::PackerEnergy  sc_probb_E 
)
unsigned int core::pack::interaction_graph::SymmOnTheFlyEdge::count_dynamic_memory ( ) const
overridevirtual
unsigned int core::pack::interaction_graph::SymmOnTheFlyEdge::count_static_memory ( ) const
overridepure virtual
ResiduePairEvalType core::pack::interaction_graph::SymmOnTheFlyEdge::eval_type ( int  node_index) const
inline
void core::pack::interaction_graph::SymmOnTheFlyEdge::force_aa_neighbors ( int  ,
int   
)
inlineoverridevirtual

fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop.

Implements core::pack::interaction_graph::FixedBBEdge.

void core::pack::interaction_graph::SymmOnTheFlyEdge::force_all_aa_neighbors ( )
inlineoverridevirtual

fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop.

Implements core::pack::interaction_graph::FixedBBEdge.

core::PackerEnergy core::pack::interaction_graph::SymmOnTheFlyEdge::get_glycine_correction ( int  which_node,
int  state 
) const
inlineprotected
core::PackerEnergy core::pack::interaction_graph::SymmOnTheFlyEdge::get_glycine_correction_for_node ( int  node_ind,
int  state 
) const
inline
SymmOnTheFlyNode const* core::pack::interaction_graph::SymmOnTheFlyEdge::get_otf_node ( int  which_node) const
inlineprotected
SymmOnTheFlyNode* core::pack::interaction_graph::SymmOnTheFlyEdge::get_otf_node ( int  which_node)
inlineprotected
SymmOnTheFlyInteractionGraph const * core::pack::interaction_graph::SymmOnTheFlyEdge::get_otf_owner ( ) const
inlineprotected
SymmOnTheFlyInteractionGraph * core::pack::interaction_graph::SymmOnTheFlyEdge::get_otf_owner ( )
inlineprotected
core::PackerEnergy core::pack::interaction_graph::SymmOnTheFlyEdge::get_proline_correction ( int  which_node,
int  state 
) const
inlineprotected
core::PackerEnergy core::pack::interaction_graph::SymmOnTheFlyEdge::get_proline_correction_for_node ( int  node_ind,
int  state 
) const
inline
bool core::pack::interaction_graph::SymmOnTheFlyEdge::get_sparse_aa_info ( int  ,
int   
) const
inlineoverridevirtual

fullfilling base class virtual member request – however, this function does not quite make sense for a symmetric otf ig, so this is just stubbed out to return true.

Implements core::pack::interaction_graph::FixedBBEdge.

core::PackerEnergy core::pack::interaction_graph::SymmOnTheFlyEdge::get_two_body_energy ( int  const,
int  const 
) const
overridepure virtual
bool core::pack::interaction_graph::SymmOnTheFlyEdge::long_range_interactions_exist ( ) const
inline
void core::pack::interaction_graph::SymmOnTheFlyEdge::note_long_range_interactions_exist ( )
inline
void core::pack::interaction_graph::SymmOnTheFlyEdge::note_short_range_interactions_exist ( )
inline
unsigned char core::pack::interaction_graph::SymmOnTheFlyEdge::residues_adjacent_for_subunit_pair ( int  which_node,
int  other_node_subunit,
int  whichnode_restypegroup,
int  othernode_restypegroup 
) const
void core::pack::interaction_graph::SymmOnTheFlyEdge::set_residues_adjacent_for_subunit_pair ( int  which_node,
int  other_node_subunit 
)
void core::pack::interaction_graph::SymmOnTheFlyEdge::set_sparse_aa_info ( ObjexxFCL::FArray2_bool const &  )
inlineoverridevirtual

fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop.

Implements core::pack::interaction_graph::FixedBBEdge.

bool core::pack::interaction_graph::SymmOnTheFlyEdge::short_range_interactions_exist ( ) const
inline

Member Data Documentation

ResiduePairEvalType core::pack::interaction_graph::SymmOnTheFlyEdge::eval_types_[2]
private

Referenced by eval_type(), and SymmOnTheFlyEdge().

utility::vector1< core::PackerEnergy > core::pack::interaction_graph::SymmOnTheFlyEdge::glycine_corrections_[2]
private
bool core::pack::interaction_graph::SymmOnTheFlyEdge::long_range_interactions_exist_
private
utility::vector1< core::PackerEnergy > core::pack::interaction_graph::SymmOnTheFlyEdge::proline_corrections_[2]
private
ObjexxFCL::FArray4D< unsigned char > core::pack::interaction_graph::SymmOnTheFlyEdge::restypegroup_adjacency_
private

Dimensions: naatypes x naatypes x n_subunits x 2 aa_adjacency( l, k, j, i ); i = 1 or 2, repesnting either the lower or upper node respectively, the residue of which lives in the asymmetric unit j = 1..n_subunits, representing the subunit of origin for the other node's residue k = amino acid type for node i l = amino acid type for the other node

Referenced by residues_adjacent_for_subunit_pair(), and set_residues_adjacent_for_subunit_pair().

bool core::pack::interaction_graph::SymmOnTheFlyEdge::short_range_interactions_exist_
private

The documentation for this class was generated from the following files: